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Comparison of 16S rRNA sequencing with biochemical testing for species-level identification of clinical isolates of Neisseria spp.

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Abstract

We aimed to compare accuracy of genus and species level identification of Neisseria spp. using biochemical testing and 16S rRNA sequence analysis. These methods were evaluated using 85 Neisseria spp. clinical isolates initially identified to the genus level by conventional biochemical tests and API NH system (Bio-Mérieux®). In 34 % (29/85), more than one possibility was given by 16S rRNA sequence analysis. In 6 % (5/85), one of the possibilities offered by 16S rRNA gene sequencing, agreed with the result given by biochemical testing. In 4 % (3/85), the same species was given by both methods. 16S rRNA gene sequencing results did not correlate well with biochemical tests.

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References

  • Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635

    Article  CAS  Google Scholar 

  • Alber D, Oberkotter M, Suerbaum S, Claus H, Frosch M, Vogel U (2001) Genetic diversity of Neisseria lactamica strains from epidemiologically defined carriers. J Clin Microbiol 39:1710–1715

    Article  CAS  Google Scholar 

  • Alexander S, Ison C (2005) Evaluation of commercial kits for the identification of Neisseria gonorrhoeae. J Med Microbiol 54:827–831

    Article  Google Scholar 

  • Barbé G, Babolat M, Boeufgras JM, Monget D, Freney J (1994) Evaluation of API NH, a new 2-hour system for identification of Neisseria and Haemophilus species and Moraxella catarrhalis in a routine clinical laboratory. J Clin Microbiol 32:187–189

    Google Scholar 

  • Barrett SJ, Sneath PH (1994) A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140:2867–2891

    Article  CAS  Google Scholar 

  • Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A (2004) Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 42:3711–3730

    Article  CAS  Google Scholar 

  • Blackwood KS, Turenne CY, Harmsen D, Kabani AM (2004) Reassessment of sequence-based targets for identification of Bacillus species. J Clin Microbiol 42:1626–1630

    Google Scholar 

  • Bosshard PP, Abels S, Zbinden R, Bottger EC, Altwegg M (2003) Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol 41:4134–4140

    Article  CAS  Google Scholar 

  • Boudewijns M, Bakkers JM, Sturm PDJ, Melchers WJG (2006) 16S rRNA gene sequencing and the routine clinical microbiology laboratory, a perfect marriage? J Clin Microbiol 44:3469–3470

    Article  Google Scholar 

  • Condon C, Liveris D, Squires C, Schwartz I, Squires CL (1995) rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J Bacteriol 177:4152–4156

    CAS  Google Scholar 

  • Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38:3623–3630

    CAS  Google Scholar 

  • Dubnau D, Smith I, Morell P, Marmur J (1965) Gene conservation in Bacillus species. Proc Natl Acad Sci USA 54:491–498

    Article  CAS  Google Scholar 

  • Euzéby JP (2007) List of prokaryotic names with standing in nomenclature-genus Neisseria, http,//www.bacterio.cict.fr/neisseria

  • Fox GE, Wisotzkey JD, Jurtshuk P Jr (1992) How close is close, 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170

    Article  CAS  Google Scholar 

  • Harris C, Perry K (2006). Neisseria spp. identification kits, a review of evaluation literature. Centre for Infections—Health Protection Agency, Report 06040

  • Hombrouck-Alet C, Poilane I, Janoir-Jouveshomme C, Fain O, Cruaud P, Thomas M, Collignon A (2003) Utilization of 16S ribosomal DNA sequencing for diagnosis of septicemia due to Neisseria elongata subsp. glycolytica in a neutropenic patient. J Clin Microbiol 41:3436–3437

    Article  CAS  Google Scholar 

  • Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V et al (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423:87–91

    Article  CAS  Google Scholar 

  • Janda JM, Abbott SL (2002) Bacterial identification for publication, when is enough enough? J Clin Microbiol 40:1887–1891

    Article  Google Scholar 

  • Janda JM, Abbott SL (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory, pluses, perils, and pitfalls. J Clin Microbiol 45:2761–2764

    Article  CAS  Google Scholar 

  • Knapp JS (1988) Historical perspectives and identification of Neisseria and related species. Clin Microbiol Rev 1:415–431

    CAS  Google Scholar 

  • Lavigne JP, Le Bayon A, Michaux Charachon S, Arich C, Bouziges N, Campello C, Sotto A (2004) Bactériémie à Neisseria subflava subsp. perflava: à propos d’un cas et revue de la littérature. Med Mal Infect 34:331–332

    Article  CAS  Google Scholar 

  • Mangold KA, Regner MA, Tajuddin M, Tajuddin AM, Jennings L, Du H, Kaul KL (2007) Neisseria species identification assay for the confirmation of Neisseria gonorrhoeae positive results of the COBAS amplicor PCR. J Clin Microbiol 45:1403–1409

    Article  CAS  Google Scholar 

  • Maynard Smith J, Smith NH, O’Rourke M, Spratt BG (1993) How clonal are bacteria? Proc Natl Acad Sci USA 90:4384–4388

    Article  Google Scholar 

  • Mechergui A, Touati A, Baaboura R, Achour W, Ben Hassen A (2011) Phenotypic and molecular characterization of β-lactams  resistance in commensal Neisseria strains isolated from neutropenic patients in Tunisia. Ann Microbiol 61:695–697

    Google Scholar 

  • Mignard S, Flandrois JP (2006) 16S rRNA sequencing in routine bacterial identification, a 30-month experiment. J Microbiol Methods 67:574–581

    Article  CAS  Google Scholar 

  • Molina F, Duran MT, Llinares P, Diz-Lois F (2000) Encocarditis due to Neisseria subflava with negative blood cultures. Clin Microbiol Newsl 22:158–159

    Article  Google Scholar 

  • Palys T, Cohan LK, Nakamura FM (1997) Discovery and classification of ecological diversity in the bacterial world, the role of DNA sequence data. Int J Syst Bacteriol 47:1145–1156

    Article  CAS  Google Scholar 

  • Petatán-Sagahón I, Anducho-Reyes MA, Silva-Rojas HV, Arana-Cuenca A, Tellez-Jurado A, Cárdenas-Álvarez IO, Mercado-Flores Y (2011) Isolation of bacteria with antifungal activity against the phytopathogenic fungi Stenocarpella maydis and Stenocarpella macrospora. Int J Mol Sci 12:5522–5537

    Article  Google Scholar 

  • Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE et al (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81–86

    Article  CAS  Google Scholar 

  • Rennie RP, Brosnikoff C, Shokoples S, Reller LB, Mirrett S, Janda W, Ristow K, Krilcich A (2008) Multicenter evaluation of the new vitek 2 Neisseria-Haemophilus identification card. J Clin Microbiol 46:2681–2685

    Article  Google Scholar 

  • Sacchi CT, Whitney AM, Mayer LW, Morey R, Steigerwalt A, Boras A, Weyant RS, Popovic T (2002a) Sequencing of 16S rRNA gene, a rapid tool for identification of Bacillus anthracis. Emerg Infect Dis 8:1117–1123

    Article  CAS  Google Scholar 

  • Sacchi CT, Whitney AM, Reeves MW, Mayer LW, Popovic T (2002b) Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool. J Clin Microbiol 40:4520–4527

    Article  CAS  Google Scholar 

  • Shetty AK, Nagaraj SK, Lorentz WB, Bitzan M (2005) Peritonitis due to Neisseria mucosa in an adolescent receiving peritoneal dialysis. Infection 33:390–392

    Article  CAS  Google Scholar 

  • Smith NH, Holmes EC, Donovan GM, Carpenter GA, Spratt BG (1999) Networks and groups within the genus Neisseria, analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol Biol Evol 16:773–783

    Article  CAS  Google Scholar 

  • Stein DC (2006) The Neisseria. In: Dworkin MM, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 602–6647

    Chapter  Google Scholar 

  • Tsai CM (2011) Lipooligosaccharides of Neisseria species, similarity between N. polysaccharea and N. meningitidis LOSs. Adv Exp Med Biol 705:381–394

    Article  CAS  Google Scholar 

  • Wilson SP (1928) An investigation of certain gram-negative cocci met with in the nasopharynx, with special reference to their classification. J Pathol Bacteriol 31:477–492

    Article  Google Scholar 

  • Wilson GS, Smith MM (1928) Observations on the gram-negative cocci of the nasopharynx, with a description of Neisseria pharyngis. J Pathol Bacteriol 31:597–608

    Article  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Mol Biol Rev 51:221–271

    CAS  Google Scholar 

  • Woese CR, Stackebrandt E, Macke TJ, Fox GE (1985) A phylogentic definition of major eubacterial taxa. Syst Appl Microbiol 6:143–151

    Article  CAS  Google Scholar 

  • Woo PCY, Ng KHI, Lau SKP, Yip KT, Fung AMY, Leung KW, Tam DMW, Que TL, Yuen KY (2003) Usefulness of the MicroSeq 500 16S ribosomal DNA-based identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J Clin Microbiol 41:1996–2001

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Service des Laboratoires (UR12ES02), Centre National de Greffe de Moelle Osseuse, Rue Djebel-Lakdhar, Bab Saadoun, 1006, Tunis, Tunisia

    Arij Mechergui, Wafa Achour & Assia Ben Hassen

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  1. Arij Mechergui
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  2. Wafa Achour
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  3. Assia Ben Hassen
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Correspondence to Arij Mechergui.

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Mechergui, A., Achour, W. & Ben Hassen, A. Comparison of 16S rRNA sequencing with biochemical testing for species-level identification of clinical isolates of Neisseria spp.. World J Microbiol Biotechnol 30, 2181–2188 (2014). https://doi.org/10.1007/s11274-014-1637-9

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  • DOI: https://doi.org/10.1007/s11274-014-1637-9

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